The probable reason why bombers hurt jar jar is because your caps always get sniped lol.. dont build caps, build hc
If the enemy is spamming enough bombers to snipe your caps before you can retreat them, countering with heavy cruisers is not a good idea, because HCs are even weaker to bombers than caps are.
I don't play ICO, and I'm glad for it. But 150 LRF w/flak & carriers vs anything else? Who will win that, I wonder?
A huge late-game fleet like that might be best countered with (a very large opposing fleet of) mostly flak. Depending on the number of enemy bombers you might want to avoid sending your own caps in altogether or they might just die to the bombers when the cap warps in.
Saying not to build caps and to build HCs is flat out ridiculous. You need the abilities the caps have to win. Like Scramble Bombers and Embargo.
Cap abilities are nice, but in the face of large enemy bomber/LRF spam they come at a very significant cost: your cap(s) will die, especially if they're at anything other than very low levels.
And when fleets are that large, Scramble Bombers and Embargo are of very little use and certainly don't come anywhere close to deciding the game. Scramble Bombers is great in the early-mid game when one or two or three extra bomber squads every 30 seconds can be a very significant boost to your anti-cap/anti-structure/anti-Orki firepower, but if you get the cap just for Scramble Bombers in the late-game you'd be much better off building normal carrier cruisers, which would simply have more strike-craft firepower per cost and supply.
And Embargo is only really that useful in the early-game, or if your enemy is very bad at fleet logistics and can't scare your Sova out of his gravity well relatively quickly. When fleets are so large to have extreme numbers of LRF or bombers, what matters is fleet firepower, not income (plus, your Sova will be focus-fired upon and will die).
Anyway, if you want strategy, cut the fleet supply in half. There's your strategy. Forces you to have to think about what you build.
Read master1a's post again. He has a point (and is one of the best players on ICO, if not the best - he knows what he's talking about).
Regardless of fleet supply, you have to make strategic decisions about what kind of ship to build, about where to position your fleet, when to move your frig factories, when to build defenses, when to retreat, when to attack an enemy's HW or to culture them to death, when to build trade ports or to feed allies, when to send a SB, when to double a dangerous player even if it means you yourself lose to the guy on the other side of you...
There is a whole lot to Sins than "1. Spam 2. Win".